3B9GA

Crystal structure of loop deletion mutant of trypanosoma vivax nucleoside hydrolase (3gtvnh) in complex with immh
Total Genus 121

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
121
sequence length
317
structure length
317
Chain Sequence
SAKNVVLDHDGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVTGKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPENVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKYGEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGCPGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMGGGYAWDALTAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAENYPLTFVARNPEAEFFLDMLLRSARAC
5010015020025030030025020015010050
020406080100120Genus Matrix

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
S1 (3-9)TI1 (25-28)AH12 (250-259)AH6 (140-156)AH2 (43-61)AH1 (13-24)AH13 (303-314)S2 (29-36)TIV1 (38-41)S3 (68-70)AH3 (85-92)AH5 (117-127)3H1 (81-83)TVIII2 (128-131)EMPTYS4 (132-136)S5 (158-164)AH7 (185-189)S6 (205-208)TI3 (167-170)TI4 (176-179)TI8 (278-281)AH8 (191-199)S7 (266-274)TI5 (200-203)AH9 (210-214)AH10 (220-227)TI6 (227-230)TI7 (229-232)AH11 (233-244)TII2 (289-292)TII1 (280-283)O1 (276-278)S8 (283-286)AH4 (99-114)TVIII1 (75-78)3H2 (94-96)TIV2 (214-217)S9 (294-298)3H3 (261-263)Updating...
connected with : NaN
publication title A Flexible Loop as a Functional Element in the Catalytic Mechanism of Nucleoside Hydrolase from Trypanosoma vivax.
pubmed doi rcsb
molecule keywords IAG-nucleoside hydrolase
molecule tags Hydrolase
source organism Trypanosoma vivax
total genus 121
structure length 317
sequence length 317
chains with identical sequence B
ec nomenclature ec 3.2.2.1: Purine nucleosidase.
pdb deposition date 2007-11-05

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01156 IU_nuc_hydro Inosine-uridine preferring nucleoside hydrolase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.245.10 Alpha Beta Alpha-Beta Complex Inosine-uridine Nucleoside N-ribohydrolase; Chain A Ribonucleoside hydrolase-like 3b9gA00
1MASA 4KPNA 2MASA 3T8IA 4P5FA 1HP0A 4KL0A 4I70A 3EPXA 3MKMA 2YHGA 1HOZA 4I75A 1Q8FA 1YOEA 3EPWA 2FF1A 3G5IA 1EZRA 4I71A 5TSQA 2FF2A 4I72A 4I73A 4WR2A 3B9GA 3T8JA 1R4FA 3MKNA 3B9XA 4KPOA 4I74A 1KIEA 1KICA 3FZ0A 2C40A
chains in the Genus database with same CATH superfamily
1MASA 4KPNA 2MASA 3T8IA 4P5FA 1HP0A 4KL0A 4I70A 3EPXA 3MKMA 2YHGA 1HOZA 4I75A 1Q8FA 1YOEA 3EPWA 2FF1A 3G5IA 1EZRA 4I71A 5TSQA 2FF2A 4I72A 4I73A 4WR2A 3B9GA 3T8JA 1R4FA 3MKNA 3B9XA 4KPOA 4I74A 1KIEA 1KICA 3FZ0A 2C40A
chains in the Genus database with same CATH topology
1MASA 4KPNA 2MASA 3T8IA 4P5FA 1HP0A 4KL0A 4I70A 3EPXA 3MKMA 2YHGA 1HOZA 4I75A 1Q8FA 1YOEA 3EPWA 2FF1A 3G5IA 1EZRA 4I71A 5TSQA 2FF2A 4I72A 4I73A 4WR2A 3B9GA 3T8JA 1R4FA 3MKNA 3B9XA 4KPOA 4I74A 1KIEA 1KICA 3FZ0A 2C40A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1MAS A;  4KPN A;  2MAS A;  3T8I A;  4P5F A;  1HP0 A;  4KL0 A;  4I70 A;  3EPX A;  3MKM A;  2YHG A;  1HOZ A;  4I75 A;  1Q8F A;  1YOE A;  3EPW A;  2FF1 A;  3G5I A;  1EZR A;  4I71 A;  5TSQ A;  2FF2 A;  4I72 A;  4I73 A;  4WR2 A;  3B9G A;  3T8J A;  1R4F A;  3MKN A;  3B9X A;  4KPO A;  4I74 A;  1KIE A;  1KIC A;  3FZ0 A;  2C40 A; 
#chains in the Genus database with same CATH topology
 1MAS A;  4KPN A;  2MAS A;  3T8I A;  4P5F A;  1HP0 A;  4KL0 A;  4I70 A;  3EPX A;  3MKM A;  2YHG A;  1HOZ A;  4I75 A;  1Q8F A;  1YOE A;  3EPW A;  2FF1 A;  3G5I A;  1EZR A;  4I71 A;  5TSQ A;  2FF2 A;  4I72 A;  4I73 A;  4WR2 A;  3B9G A;  3T8J A;  1R4F A;  3MKN A;  3B9X A;  4KPO A;  4I74 A;  1KIE A;  1KIC A;  3FZ0 A;  2C40 A; 
#chains in the Genus database with same CATH homology
 1MAS A;  4KPN A;  2MAS A;  3T8I A;  4P5F A;  1HP0 A;  4KL0 A;  4I70 A;  3EPX A;  3MKM A;  2YHG A;  1HOZ A;  4I75 A;  1Q8F A;  1YOE A;  3EPW A;  2FF1 A;  3G5I A;  1EZR A;  4I71 A;  5TSQ A;  2FF2 A;  4I72 A;  4I73 A;  4WR2 A;  3B9G A;  3T8J A;  1R4F A;  3MKN A;  3B9X A;  4KPO A;  4I74 A;  1KIE A;  1KIC A;  3FZ0 A;  2C40 A; 
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similar chains in the pdb database (?% sequence similarity)

 
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